AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0973030


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0973030 MtrunA17_Chr6g0451941 98.013 151 3 0 1 151 1 151 7.32e-110 308
Msa0973030 MtrunA17_Chr7g0262351 34.513 113 73 1 25 137 14 125 4.67e-18 75.5
Msa0973030 MtrunA17_Chr8g0364781 35.185 108 68 1 33 138 12 119 7.21e-16 69.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0973030 AT5G26594.1 32.143 112 76 0 33 144 18 129 3.88e-18 75.9

Find 30 sgRNAs with CRISPR-Local

Find 126 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCTCTCGGGTCAAAGGTTT+TGG 0.182755 6_4:-5353319 None:intergenic
TACCTCGGGTCCATTGATTA+TGG 0.250485 6_4:-5352626 None:intergenic
AGCAATGCATTCATTGGATA+TGG 0.328332 6_4:-5352451 None:intergenic
GCTTCTTGAGCACTATTTGC+AGG 0.339727 6_4:-5352544 None:intergenic
CACTATTTGCAGGCTCTGTT+CGG 0.378455 6_4:-5352534 None:intergenic
CATCATATGCTTGAATCAAT+AGG 0.390164 6_4:+5352508 Msa0973030:CDS
TTTGATTTGCCCATAATCAA+TGG 0.409566 6_4:+5352616 Msa0973030:CDS
GAGAGTTTCGTGTTCATCAC+TGG 0.412225 6_4:+5353337 Msa0973030:CDS
GATCAAAATGTGCAAATGTT+TGG 0.412226 6_4:+5353271 Msa0973030:CDS
ACCTCGGGTCCATTGATTAT+GGG 0.437317 6_4:-5352625 None:intergenic
TCTACTAGCAATGCATTCAT+TGG 0.442738 6_4:-5352457 None:intergenic
GTGAGGCAGATGCGTGCAAT+GGG 0.459873 6_4:+5353208 Msa0973030:CDS
CATATGATGCTCTAAGCGTC+TGG 0.510351 6_4:-5352494 None:intergenic
TGATGAACACGAAACTCTCT+CGG 0.514124 6_4:-5353333 None:intergenic
ACGAAACTCTCTCGGGTCAA+AGG 0.520328 6_4:-5353325 None:intergenic
ATGAATGCATTGCTAGTAGA+TGG 0.528865 6_4:+5352460 Msa0973030:CDS
AGAGTTTCGTGTTCATCACT+GGG 0.560420 6_4:+5353338 Msa0973030:CDS
GATGAACACGAAACTCTCTC+GGG 0.564888 6_4:-5353332 None:intergenic
AAGTTGCAATCAACAATGGA+TGG 0.566106 6_4:+5352349 None:intergenic
GGGATACAGAGCAAGGTGGT+TGG 0.588650 6_4:+5353229 Msa0973030:CDS
GGTGAGGCAGATGCGTGCAA+TGG 0.598157 6_4:+5353207 Msa0973030:CDS
AACAATGGATGGAGGAACCA+CGG 0.600766 6_4:+5352360 None:intergenic
ATCTGCATTAGTTTCACATG+CGG 0.612322 6_4:-5353369 None:intergenic
TGCAATGGGGATACAGAGCA+AGG 0.629234 6_4:+5353222 Msa0973030:CDS
ACAATGGATGGAGGAACCAC+GGG 0.635016 6_4:+5352361 None:intergenic
GCCCATAATCAATGGACCCG+AGG 0.655096 6_4:+5352624 Msa0973030:CDS
GAGGAACCACGGGATATAAG+CGG 0.658571 6_4:+5352371 Msa0973030:CDS
TTGCAATCAACAATGGATGG+AGG 0.668830 6_4:+5352352 None:intergenic
TGAGGCAGATGCGTGCAATG+GGG 0.781176 6_4:+5353209 Msa0973030:CDS
AATGGGGATACAGAGCAAGG+TGG 0.782718 6_4:+5353225 Msa0973030:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTACTTATATATTAACTAT+TGG + chr6_4:5352825-5352844 Msa0973030:intron 10.0%
!! ATTACTTATATATTAACTAT+TGG + chr6_4:5352825-5352844 Msa0973030:intron 10.0%
!!! TAAATAAATTTTTGATACCT+CGG - chr6_4:5352644-5352663 None:intergenic 15.0%
!!! AATATATAAGTAATTTTGTC+CGG - chr6_4:5352819-5352838 None:intergenic 15.0%
!!! TAAATAAATTTTTGATACCT+CGG - chr6_4:5352644-5352663 None:intergenic 15.0%
!!! AATATATAAGTAATTTTGTC+CGG - chr6_4:5352819-5352838 None:intergenic 15.0%
!!! AAATAAATTTTTGATACCTC+GGG - chr6_4:5352643-5352662 None:intergenic 20.0%
!!! ATATATAAGTAATTTTGTCC+GGG - chr6_4:5352818-5352837 None:intergenic 20.0%
!! ACTTATATATTAACTATTGG+TGG + chr6_4:5352828-5352847 Msa0973030:intron 20.0%
!! TAAAATTGACAACTCATTTA+TGG - chr6_4:5353117-5353136 None:intergenic 20.0%
!!! AAATAAATTTTTGATACCTC+GGG - chr6_4:5352643-5352662 None:intergenic 20.0%
!!! ATATATAAGTAATTTTGTCC+GGG - chr6_4:5352818-5352837 None:intergenic 20.0%
!! ACTTATATATTAACTATTGG+TGG + chr6_4:5352828-5352847 Msa0973030:intron 20.0%
!! TAAAATTGACAACTCATTTA+TGG - chr6_4:5353117-5353136 None:intergenic 20.0%
!! CAACTAGTTAGTTTAAAATG+TGG - chr6_4:5352700-5352719 None:intergenic 25.0%
! TTAATCTCATATTTAGACTG+TGG + chr6_4:5352749-5352768 Msa0973030:intron 25.0%
! TAATCTCATATTTAGACTGT+GGG + chr6_4:5352750-5352769 Msa0973030:intron 25.0%
!!! GGATCTATTTTGATCATATA+TGG - chr6_4:5352955-5352974 None:intergenic 25.0%
!!! TTCCTAATTACTTTTGTAGT+TGG + chr6_4:5353186-5353205 Msa0973030:intron 25.0%
!! CAACTAGTTAGTTTAAAATG+TGG - chr6_4:5352700-5352719 None:intergenic 25.0%
! TTAATCTCATATTTAGACTG+TGG + chr6_4:5352749-5352768 Msa0973030:intron 25.0%
! TAATCTCATATTTAGACTGT+GGG + chr6_4:5352750-5352769 Msa0973030:intron 25.0%
!!! GGATCTATTTTGATCATATA+TGG - chr6_4:5352955-5352974 None:intergenic 25.0%
!!! TTCCTAATTACTTTTGTAGT+TGG + chr6_4:5353186-5353205 Msa0973030:intron 25.0%
CATCATATGCTTGAATCAAT+AGG + chr6_4:5352508-5352527 Msa0973030:CDS 30.0%
!! TTTGATTTGCCCATAATCAA+TGG + chr6_4:5352616-5352635 Msa0973030:CDS 30.0%
TGAGATGAATTCTTATCATC+TGG + chr6_4:5352898-5352917 Msa0973030:intron 30.0%
!!! TCATCTGGACTATTTTTTGT+TGG + chr6_4:5352913-5352932 Msa0973030:intron 30.0%
ATCCTTTGTCATCAACTTTA+TGG + chr6_4:5352971-5352990 Msa0973030:intron 30.0%
!! TACCATAAAGTTGATGACAA+AGG - chr6_4:5352976-5352995 None:intergenic 30.0%
ATTTATGGACTTGGATTTGA+CGG - chr6_4:5353102-5353121 None:intergenic 30.0%
CACCAACTACAAAAGTAATT+AGG - chr6_4:5353191-5353210 None:intergenic 30.0%
!! AATTACTTTTGTAGTTGGTG+AGG + chr6_4:5353191-5353210 Msa0973030:intron 30.0%
GATCAAAATGTGCAAATGTT+TGG + chr6_4:5353271-5353290 Msa0973030:CDS 30.0%
CATCATATGCTTGAATCAAT+AGG + chr6_4:5352508-5352527 Msa0973030:CDS 30.0%
!! TTTGATTTGCCCATAATCAA+TGG + chr6_4:5352616-5352635 Msa0973030:CDS 30.0%
TGAGATGAATTCTTATCATC+TGG + chr6_4:5352898-5352917 Msa0973030:intron 30.0%
!!! TCATCTGGACTATTTTTTGT+TGG + chr6_4:5352913-5352932 Msa0973030:intron 30.0%
ATCCTTTGTCATCAACTTTA+TGG + chr6_4:5352971-5352990 Msa0973030:intron 30.0%
!! TACCATAAAGTTGATGACAA+AGG - chr6_4:5352976-5352995 None:intergenic 30.0%
ATTTATGGACTTGGATTTGA+CGG - chr6_4:5353102-5353121 None:intergenic 30.0%
CACCAACTACAAAAGTAATT+AGG - chr6_4:5353191-5353210 None:intergenic 30.0%
!! AATTACTTTTGTAGTTGGTG+AGG + chr6_4:5353191-5353210 Msa0973030:intron 30.0%
GATCAAAATGTGCAAATGTT+TGG + chr6_4:5353271-5353290 Msa0973030:CDS 30.0%
AACCTGAGGAGAAAAAAATG+TGG + chr6_4:5352401-5352420 Msa0973030:CDS 35.0%
!!! ATCCACATTTTTTTCTCCTC+AGG - chr6_4:5352406-5352425 None:intergenic 35.0%
AGCAATGCATTCATTGGATA+TGG - chr6_4:5352454-5352473 None:intergenic 35.0%
TCTACTAGCAATGCATTCAT+TGG - chr6_4:5352460-5352479 None:intergenic 35.0%
ATGAATGCATTGCTAGTAGA+TGG + chr6_4:5352460-5352479 Msa0973030:CDS 35.0%
ATATTTAGACTGTGGGTCTT+TGG + chr6_4:5352757-5352776 Msa0973030:intron 35.0%
TATTTAGACTGTGGGTCTTT+GGG + chr6_4:5352758-5352777 Msa0973030:intron 35.0%
TCTCATGTATCTCTTTGTTC+TGG - chr6_4:5352788-5352807 None:intergenic 35.0%
TATCTCATAGCTGAACTATC+TGG - chr6_4:5353008-5353027 None:intergenic 35.0%
AATCAAACAACCTCACTTGA+TGG + chr6_4:5353046-5353065 Msa0973030:intron 35.0%
TGACAACTCATTTATGGACT+TGG - chr6_4:5353111-5353130 None:intergenic 35.0%
AACCTGAGGAGAAAAAAATG+TGG + chr6_4:5352401-5352420 Msa0973030:CDS 35.0%
!!! ATCCACATTTTTTTCTCCTC+AGG - chr6_4:5352406-5352425 None:intergenic 35.0%
AGCAATGCATTCATTGGATA+TGG - chr6_4:5352454-5352473 None:intergenic 35.0%
TCTACTAGCAATGCATTCAT+TGG - chr6_4:5352460-5352479 None:intergenic 35.0%
ATGAATGCATTGCTAGTAGA+TGG + chr6_4:5352460-5352479 Msa0973030:CDS 35.0%
ATATTTAGACTGTGGGTCTT+TGG + chr6_4:5352757-5352776 Msa0973030:intron 35.0%
TATTTAGACTGTGGGTCTTT+GGG + chr6_4:5352758-5352777 Msa0973030:intron 35.0%
TCTCATGTATCTCTTTGTTC+TGG - chr6_4:5352788-5352807 None:intergenic 35.0%
TATCTCATAGCTGAACTATC+TGG - chr6_4:5353008-5353027 None:intergenic 35.0%
AATCAAACAACCTCACTTGA+TGG + chr6_4:5353046-5353065 Msa0973030:intron 35.0%
TGACAACTCATTTATGGACT+TGG - chr6_4:5353111-5353130 None:intergenic 35.0%
TAAGCGGCAAAAAAAACCTG+AGG + chr6_4:5352387-5352406 Msa0973030:CDS 40.0%
! GCGATGCAAATTTTGTTGAC+TGG + chr6_4:5352565-5352584 Msa0973030:CDS 40.0%
TGATGAACACGAAACTCTCT+CGG - chr6_4:5353336-5353355 None:intergenic 40.0%
AGAGTTTCGTGTTCATCACT+GGG + chr6_4:5353338-5353357 Msa0973030:CDS 40.0%
TAAGCGGCAAAAAAAACCTG+AGG + chr6_4:5352387-5352406 Msa0973030:CDS 40.0%
! GCGATGCAAATTTTGTTGAC+TGG + chr6_4:5352565-5352584 Msa0973030:CDS 40.0%
TGATGAACACGAAACTCTCT+CGG - chr6_4:5353336-5353355 None:intergenic 40.0%
AGAGTTTCGTGTTCATCACT+GGG + chr6_4:5353338-5353357 Msa0973030:CDS 40.0%
!! TTTTTGCCGCTTATATCCCG+TGG - chr6_4:5352380-5352399 None:intergenic 45.0%
! CATATGATGCTCTAAGCGTC+TGG - chr6_4:5352497-5352516 None:intergenic 45.0%
CACTATTTGCAGGCTCTGTT+CGG - chr6_4:5352537-5352556 None:intergenic 45.0%
GCTTCTTGAGCACTATTTGC+AGG - chr6_4:5352547-5352566 None:intergenic 45.0%
! ACCTCGGGTCCATTGATTAT+GGG - chr6_4:5352628-5352647 None:intergenic 45.0%
! TACCTCGGGTCCATTGATTA+TGG - chr6_4:5352629-5352648 None:intergenic 45.0%
GATACATGAGACTCAGATCC+CGG + chr6_4:5352797-5352816 Msa0973030:intron 45.0%
TGGTATCCTCATACTGACGA+TGG + chr6_4:5352848-5352867 Msa0973030:intron 45.0%
GGTATCCTCATACTGACGAT+GGG + chr6_4:5352849-5352868 Msa0973030:intron 45.0%
TGAAACCCATCGTCAGTATG+AGG - chr6_4:5352857-5352876 None:intergenic 45.0%
! CAAGTTGACTCCATCAAGTG+AGG - chr6_4:5353059-5353078 None:intergenic 45.0%
! TCTCTCGGGTCAAAGGTTTT+GGG - chr6_4:5353321-5353340 None:intergenic 45.0%
GATGAACACGAAACTCTCTC+GGG - chr6_4:5353335-5353354 None:intergenic 45.0%
GAGAGTTTCGTGTTCATCAC+TGG + chr6_4:5353337-5353356 Msa0973030:CDS 45.0%
!! TTTTTGCCGCTTATATCCCG+TGG - chr6_4:5352380-5352399 None:intergenic 45.0%
! CATATGATGCTCTAAGCGTC+TGG - chr6_4:5352497-5352516 None:intergenic 45.0%
CACTATTTGCAGGCTCTGTT+CGG - chr6_4:5352537-5352556 None:intergenic 45.0%
GCTTCTTGAGCACTATTTGC+AGG - chr6_4:5352547-5352566 None:intergenic 45.0%
! ACCTCGGGTCCATTGATTAT+GGG - chr6_4:5352628-5352647 None:intergenic 45.0%
! TACCTCGGGTCCATTGATTA+TGG - chr6_4:5352629-5352648 None:intergenic 45.0%
GATACATGAGACTCAGATCC+CGG + chr6_4:5352797-5352816 Msa0973030:intron 45.0%
TGGTATCCTCATACTGACGA+TGG + chr6_4:5352848-5352867 Msa0973030:intron 45.0%
GGTATCCTCATACTGACGAT+GGG + chr6_4:5352849-5352868 Msa0973030:intron 45.0%
TGAAACCCATCGTCAGTATG+AGG - chr6_4:5352857-5352876 None:intergenic 45.0%
! CAAGTTGACTCCATCAAGTG+AGG - chr6_4:5353059-5353078 None:intergenic 45.0%
! TCTCTCGGGTCAAAGGTTTT+GGG - chr6_4:5353321-5353340 None:intergenic 45.0%
GATGAACACGAAACTCTCTC+GGG - chr6_4:5353335-5353354 None:intergenic 45.0%
GAGAGTTTCGTGTTCATCAC+TGG + chr6_4:5353337-5353356 Msa0973030:CDS 45.0%
GAGGAACCACGGGATATAAG+CGG + chr6_4:5352371-5352390 Msa0973030:CDS 50.0%
TGCAATGGGGATACAGAGCA+AGG + chr6_4:5353222-5353241 Msa0973030:CDS 50.0%
AATGGGGATACAGAGCAAGG+TGG + chr6_4:5353225-5353244 Msa0973030:CDS 50.0%
! CTCTCGGGTCAAAGGTTTTG+GGG - chr6_4:5353320-5353339 None:intergenic 50.0%
! CTCTCTCGGGTCAAAGGTTT+TGG - chr6_4:5353322-5353341 None:intergenic 50.0%
ACGAAACTCTCTCGGGTCAA+AGG - chr6_4:5353328-5353347 None:intergenic 50.0%
GAGGAACCACGGGATATAAG+CGG + chr6_4:5352371-5352390 Msa0973030:CDS 50.0%
TGCAATGGGGATACAGAGCA+AGG + chr6_4:5353222-5353241 Msa0973030:CDS 50.0%
AATGGGGATACAGAGCAAGG+TGG + chr6_4:5353225-5353244 Msa0973030:CDS 50.0%
! CTCTCGGGTCAAAGGTTTTG+GGG - chr6_4:5353320-5353339 None:intergenic 50.0%
! CTCTCTCGGGTCAAAGGTTT+TGG - chr6_4:5353322-5353341 None:intergenic 50.0%
ACGAAACTCTCTCGGGTCAA+AGG - chr6_4:5353328-5353347 None:intergenic 50.0%
GCCCATAATCAATGGACCCG+AGG + chr6_4:5352624-5352643 Msa0973030:CDS 55.0%
GTGAGGCAGATGCGTGCAAT+GGG + chr6_4:5353208-5353227 Msa0973030:CDS 55.0%
TGAGGCAGATGCGTGCAATG+GGG + chr6_4:5353209-5353228 Msa0973030:CDS 55.0%
GGGATACAGAGCAAGGTGGT+TGG + chr6_4:5353229-5353248 Msa0973030:CDS 55.0%
!!! GGTCAAAGGTTTTGGGGTGC+TGG - chr6_4:5353314-5353333 None:intergenic 55.0%
GCCCATAATCAATGGACCCG+AGG + chr6_4:5352624-5352643 Msa0973030:CDS 55.0%
GTGAGGCAGATGCGTGCAAT+GGG + chr6_4:5353208-5353227 Msa0973030:CDS 55.0%
TGAGGCAGATGCGTGCAATG+GGG + chr6_4:5353209-5353228 Msa0973030:CDS 55.0%
GGGATACAGAGCAAGGTGGT+TGG + chr6_4:5353229-5353248 Msa0973030:CDS 55.0%
!!! GGTCAAAGGTTTTGGGGTGC+TGG - chr6_4:5353314-5353333 None:intergenic 55.0%
GGTGAGGCAGATGCGTGCAA+TGG + chr6_4:5353207-5353226 Msa0973030:CDS 60.0%
GGTGAGGCAGATGCGTGCAA+TGG + chr6_4:5353207-5353226 Msa0973030:CDS 60.0%
Chromosome Type Strat End Strand Name
chr6_4 gene 5352364 5353378 5352364 ID=Msa0973030;Name=Msa0973030
chr6_4 mRNA 5352364 5353378 5352364 ID=Msa0973030-mRNA-1;Parent=Msa0973030;Name=Msa0973030-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|0|0|1|1|1|2|0|151
chr6_4 exon 5352364 5352645 5352364 ID=Msa0973030-mRNA-1:exon:2273;Parent=Msa0973030-mRNA-1
chr6_4 exon 5353205 5353378 5353205 ID=Msa0973030-mRNA-1:exon:2274;Parent=Msa0973030-mRNA-1
chr6_4 CDS 5352364 5352645 5352364 ID=Msa0973030-mRNA-1:cds;Parent=Msa0973030-mRNA-1
chr6_4 CDS 5353205 5353378 5353205 ID=Msa0973030-mRNA-1:cds;Parent=Msa0973030-mRNA-1
Gene Sequence

>Msa0973030

ATGGATGGAGGAACCACGGGATATAAGCGGCAAAAAAAACCTGAGGAGAAAAAAATGTGGATCAAAAAGCGTGAAATATATGACACTCCATATCCAATGAATGCATTGCTAGTAGATGGTGCGACTGCAACCAGACGCTTAGAGCATCATATGCTTGAATCAATAGGCATCCGAACAGAGCCTGCAAATAGTGCTCAAGAAGCGATGCAAATTTTGTTGACTGGTGTCAAATTTGACTTCATATTTGTTGATTTTGATTTGCCCATAATCAATGGACCCGAGTTGGTGAGGCAGATGCGTGCAATGGGGATACAGAGCAAGGTGGTTGGTATGTTAACAAACTTCAATGATCAAAATGTGCAAATGTTTGGAGAAGCAAGAGCTAATGCCAGCACCCCAAAACCTTTGACCCGAGAGAGTTTCGTGTTCATCACTGGGATCTTGCGCCGCATGTGA

Protein sequence

>Msa0973030

MDGGTTGYKRQKKPEEKKMWIKKREIYDTPYPMNALLVDGATATRRLEHHMLESIGIRTEPANSAQEAMQILLTGVKFDFIFVDFDLPIINGPELVRQMRAMGIQSKVVGMLTNFNDQNVQMFGEARANASTPKPLTRESFVFITGILRRM*